I am running 12.04 64-bit and am dual booting with Win7, for full disclosure, although I suspect that has nothing to do with my problem.

The boot-loader(GRUB) fails to load often and I will be presented with a black screen with a single blinking line. This has happened to me eight out of ten power cycles now and I can fix it consistently, however, I have no idea why it happens.

My current fix is to boot a live CD (I've tried both KNOPPIX and Ubuntu with the same result) and that's it. Somehow booting with the live CD is enough to "wake-up" my hard drive. I then reboot and GRUB magically appears again.

So what is going on? Is it possible that a program is corrupting my MBR and the live CD is restoring it? How can I narrow down the possibilities? Thanks.

Additional

This is still a problem. I'm convinced now that it is not hardware related as I've spent the last month and several boot cycles on Windows without a hiccup. Recently when I started using Ubuntu again the problem started again.

I am more interested in figuring out what is going on rather than actually fixing the problem. Are there any tools, logs, etc. I can use to unravel this mystery?

Update

I can now consistently recreate the issue. It seems that if the computer is put into suspend mode at any point prior to restarting, the problem comes up. The computer goes into and out of suspend mode just fine but when I restart the system it fails to boot. I've tried this command before and after suspending the computer:

sudo hdparm -I /dev/sda > hdsettings.txt

Then I ran a diff on the two files and found that one thing changed: under security settings frozen changed to not frozen. I have no idea what that means but it's a difference anyhow.

I'm still having this problem and I am still able to repair it by simply booting a live CD. I don't think it's hardware just because of how reproducible the fix is. Is there a log file I can print out from the live boot CD?
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UsagiSep 5 '12 at 6:53

I had a similar problem not long ago. I was using a hard drive I took from a DVR I wasn't using. These drives use a custom firmware with a feature called Power-up in Standby mode which prevents the drive from drawing too much current at boot time; the custom firmware then sends a special command to the drive to get it spinning. This can be prevented by restarting the computer or you can disable the feature from the drive completely using hdparm. The drive will then be in active mode.

I don't know if my hard-drive has this feature but I've been reading the manual now for hdparm and It's pretty useful :D Also, in trying all of this out I found out that the problem is suspend related. I haven't fixed the problem but I'm one step closer!
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UsagiDec 24 '12 at 10:54

According to other people who got this error, it was solved by changing the jumper configuration of the drive. Does your drive have any jumpers? If so, what is the setting?
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francismbDec 24 '12 at 15:47

It does. I just tried all of the positions to no avail. I'm thinking that my drive doesn't have this option. Are there other power management features I can change either on the drive or through Linux?
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UsagiDec 25 '12 at 3:45